//
// Manta - Structural Variant and Indel Caller
// Copyright (c) 2013-2019 Illumina, Inc.
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program.  If not, see <http://www.gnu.org/licenses/>.
//
//

#include "bam_header_info.hpp"

#include <iostream>

bam_header_info::bam_header_info(const bam_hdr_t& header)
{
  for (int i(0); i < header.n_targets; ++i) {
    chrom_data.emplace_back(header.target_name[i], header.target_len[i]);
    chrom_to_index[header.target_name[i]] = (int32_t)i;
  }
}

std::ostream& operator<<(std::ostream& os, const bam_header_info& bhi)
{
  unsigned index(0);

  os << "chomosome_id_map:\n";
  for (const bam_header_info::chrom_info& info : bhi.chrom_data) {
    os << "index: " << index << " label: " << info.label << " length: " << info.length << '\n';
    index++;
  }
  return os;
}
